Stimulation experiments
Analysis of stimulation experiments.
library(Seurat)
library(dplyr)
library(ggplot2)
library(scClustViz)Loading required package: shinyLoad integrated object. This object has been integrated with CCA, because there was lots of batch effect between the 0hr tissue and the other two experiments (which merged quite well).
load("~/Dropbox/Zoe/scf_version/analysis/healthy_sc/seurat_objects/no_dropletQC/3391/integrated_3391_stimulation_pmaio_unstim_downsampled_cca_kanchor5_scClustViz.RData")
# Set identity
Idents(scSeurat) <- "integrated_snn_res.0.4"Check out the UMAP of clusters, original identities, and refined SCINA labels.
DimPlot(scSeurat, label = TRUE)
DimPlot(scSeurat, group.by = "tissue_type", label = FALSE)
DimPlot(scSeurat, group.by = "scina_labels", label = TRUE) & NoLegend()
pdf(file = './figures/stimulation/downsampled_UMAP.pdf')
DimPlot(scSeurat, label = TRUE)
dev.off()null device
1 pdf(file = './figures/stimulation/downsampled_tissue_type_UMAP.pdf')DimPlot(scSeurat, group.by = "tissue_type") +
ggtitle(NULL)
dev.off()null device
1 Look at tissue-type per cluster on a proportional level:
pt <- table(Idents(scSeurat), scSeurat$tissue_type)
pt <- as.data.frame(pt)
plot <- ggplot(pt, aes(x = Var1, y = Freq, fill = Var2)) +
theme_bw(base_size = 15) +
geom_col(position = "fill", width = 0.5) +
xlab("Sample") +
ylab("Proportion") +
theme(legend.title = element_blank())
plot
pdf(file = './figures/stimulation/downsampled_tissue_type_barplot.pdf')plot
dev.off()png
2 
Calculate all DE genes
all.markers <- FindAllMarkers(scSeurat,
only.pos = TRUE,
min.pct = 0.25,
logfc.threshold = 0.25,
recorrect_umi = FALSE)Calculating cluster 0
| | 0 % ~calculating
|+ | 1 % ~05s
|++ | 2 % ~05s
|++ | 3 % ~05s
|+++ | 4 % ~05s
|+++ | 5 % ~05s
|++++ | 6 % ~05s
|++++ | 7 % ~05s
|+++++ | 8 % ~05s
|+++++ | 9 % ~05s
|++++++ | 11% ~05s
|++++++ | 12% ~04s
|+++++++ | 13% ~04s
|+++++++ | 14% ~04s
|++++++++ | 15% ~04s
|++++++++ | 16% ~04s
|+++++++++ | 17% ~04s
|+++++++++ | 18% ~04s
|++++++++++ | 19% ~04s
|++++++++++ | 20% ~04s
|+++++++++++ | 21% ~04s
|++++++++++++ | 22% ~04s
|++++++++++++ | 23% ~04s
|+++++++++++++ | 24% ~04s
|+++++++++++++ | 25% ~04s
|++++++++++++++ | 26% ~04s
|++++++++++++++ | 27% ~04s
|+++++++++++++++ | 28% ~04s
|+++++++++++++++ | 29% ~04s
|++++++++++++++++ | 31% ~04s
|++++++++++++++++ | 32% ~04s
|+++++++++++++++++ | 33% ~03s
|+++++++++++++++++ | 34% ~03s
|++++++++++++++++++ | 35% ~03s
|++++++++++++++++++ | 36% ~03s
|+++++++++++++++++++ | 37% ~03s
|+++++++++++++++++++ | 38% ~03s
|++++++++++++++++++++ | 39% ~03s
|++++++++++++++++++++ | 40% ~03s
|+++++++++++++++++++++ | 41% ~03s
|++++++++++++++++++++++ | 42% ~03s
|++++++++++++++++++++++ | 43% ~03s
|+++++++++++++++++++++++ | 44% ~03s
|+++++++++++++++++++++++ | 45% ~03s
|++++++++++++++++++++++++ | 46% ~03s
|++++++++++++++++++++++++ | 47% ~03s
|+++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|++++++++++++++++++++++++++ | 52% ~02s
|+++++++++++++++++++++++++++ | 53% ~02s
|+++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 55% ~02s
|++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|+++++++++++++++++++++++++++++ | 58% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 61% ~02s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~02s
|+++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|++++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|+++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~01s
|++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|+++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05s Calculating cluster 1
| | 0 % ~calculating
|+ | 1 % ~06s
|++ | 2 % ~06s
|++ | 4 % ~06s
|+++ | 5 % ~06s
|+++ | 6 % ~06s
|++++ | 7 % ~06s
|+++++ | 8 % ~06s
|+++++ | 10% ~06s
|++++++ | 11% ~06s
|++++++ | 12% ~06s
|+++++++ | 13% ~06s
|++++++++ | 14% ~06s
|++++++++ | 15% ~05s
|+++++++++ | 17% ~05s
|+++++++++ | 18% ~05s
|++++++++++ | 19% ~05s
|+++++++++++ | 20% ~05s
|+++++++++++ | 21% ~05s
|++++++++++++ | 23% ~05s
|++++++++++++ | 24% ~05s
|+++++++++++++ | 25% ~05s
|++++++++++++++ | 26% ~05s
|++++++++++++++ | 27% ~05s
|+++++++++++++++ | 29% ~05s
|+++++++++++++++ | 30% ~05s
|++++++++++++++++ | 31% ~04s
|+++++++++++++++++ | 32% ~04s
|+++++++++++++++++ | 33% ~04s
|++++++++++++++++++ | 35% ~04s
|++++++++++++++++++ | 36% ~04s
|+++++++++++++++++++ | 37% ~04s
|++++++++++++++++++++ | 38% ~04s
|++++++++++++++++++++ | 39% ~04s
|+++++++++++++++++++++ | 40% ~04s
|+++++++++++++++++++++ | 42% ~04s
|++++++++++++++++++++++ | 43% ~04s
|+++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|++++++++++++++++++++++++ | 46% ~03s
|++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|+++++++++++++++++++++++++ | 50% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|+++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~03s
|++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|++++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|+++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~02s
|+++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06s Calculating cluster 2
| | 0 % ~calculating
|+ | 1 % ~03s
|++ | 2 % ~03s
|++ | 4 % ~03s
|+++ | 5 % ~03s
|+++ | 6 % ~03s
|++++ | 7 % ~03s
|+++++ | 8 % ~03s
|+++++ | 10% ~03s
|++++++ | 11% ~03s
|++++++ | 12% ~03s
|+++++++ | 13% ~03s
|++++++++ | 14% ~03s
|++++++++ | 15% ~03s
|+++++++++ | 17% ~03s
|+++++++++ | 18% ~03s
|++++++++++ | 19% ~03s
|+++++++++++ | 20% ~02s
|+++++++++++ | 21% ~02s
|++++++++++++ | 23% ~02s
|++++++++++++ | 24% ~02s
|+++++++++++++ | 25% ~02s
|++++++++++++++ | 26% ~02s
|++++++++++++++ | 27% ~02s
|+++++++++++++++ | 29% ~02s
|+++++++++++++++ | 30% ~02s
|++++++++++++++++ | 31% ~02s
|+++++++++++++++++ | 32% ~02s
|+++++++++++++++++ | 33% ~02s
|++++++++++++++++++ | 35% ~02s
|++++++++++++++++++ | 36% ~02s
|+++++++++++++++++++ | 37% ~02s
|++++++++++++++++++++ | 38% ~02s
|++++++++++++++++++++ | 39% ~02s
|+++++++++++++++++++++ | 40% ~02s
|+++++++++++++++++++++ | 42% ~02s
|++++++++++++++++++++++ | 43% ~02s
|+++++++++++++++++++++++ | 44% ~02s
|+++++++++++++++++++++++ | 45% ~02s
|++++++++++++++++++++++++ | 46% ~02s
|++++++++++++++++++++++++ | 48% ~02s
|+++++++++++++++++++++++++ | 49% ~02s
|+++++++++++++++++++++++++ | 50% ~02s
|++++++++++++++++++++++++++ | 51% ~02s
|+++++++++++++++++++++++++++ | 52% ~01s
|+++++++++++++++++++++++++++ | 54% ~01s
|++++++++++++++++++++++++++++ | 55% ~01s
|++++++++++++++++++++++++++++ | 56% ~01s
|+++++++++++++++++++++++++++++ | 57% ~01s
|++++++++++++++++++++++++++++++ | 58% ~01s
|++++++++++++++++++++++++++++++ | 60% ~01s
|+++++++++++++++++++++++++++++++ | 61% ~01s
|+++++++++++++++++++++++++++++++ | 62% ~01s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|+++++++++++++++++++++++++++++++++ | 64% ~01s
|+++++++++++++++++++++++++++++++++ | 65% ~01s
|++++++++++++++++++++++++++++++++++ | 67% ~01s
|++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 69% ~01s
|++++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 71% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|+++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~00s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~00s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=03s Calculating cluster 3
| | 0 % ~calculating
|+ | 1 % ~07s
|++ | 2 % ~07s
|++ | 3 % ~06s
|+++ | 5 % ~06s
|+++ | 6 % ~06s
|++++ | 7 % ~06s
|+++++ | 8 % ~06s
|+++++ | 9 % ~06s
|++++++ | 10% ~06s
|++++++ | 11% ~06s
|+++++++ | 13% ~06s
|+++++++ | 14% ~06s
|++++++++ | 15% ~06s
|+++++++++ | 16% ~06s
|+++++++++ | 17% ~06s
|++++++++++ | 18% ~05s
|++++++++++ | 20% ~05s
|+++++++++++ | 21% ~05s
|+++++++++++ | 22% ~05s
|++++++++++++ | 23% ~05s
|+++++++++++++ | 24% ~05s
|+++++++++++++ | 25% ~05s
|++++++++++++++ | 26% ~05s
|++++++++++++++ | 28% ~05s
|+++++++++++++++ | 29% ~05s
|+++++++++++++++ | 30% ~05s
|++++++++++++++++ | 31% ~05s
|+++++++++++++++++ | 32% ~05s
|+++++++++++++++++ | 33% ~04s
|++++++++++++++++++ | 34% ~04s
|++++++++++++++++++ | 36% ~04s
|+++++++++++++++++++ | 37% ~04s
|+++++++++++++++++++ | 38% ~04s
|++++++++++++++++++++ | 39% ~04s
|+++++++++++++++++++++ | 40% ~04s
|+++++++++++++++++++++ | 41% ~04s
|++++++++++++++++++++++ | 43% ~04s
|++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|+++++++++++++++++++++++ | 46% ~04s
|++++++++++++++++++++++++ | 47% ~04s
|+++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 53% ~03s
|++++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~03s
|+++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 57% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|++++++++++++++++++++++++++++++++ | 62% ~03s
|++++++++++++++++++++++++++++++++ | 63% ~02s
|+++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|+++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=07s Calculating cluster 4
| | 0 % ~calculating
|+ | 1 % ~04s
|++ | 3 % ~04s
|++ | 4 % ~04s
|+++ | 5 % ~03s
|++++ | 7 % ~03s
|++++ | 8 % ~03s
|+++++ | 9 % ~03s
|++++++ | 11% ~03s
|++++++ | 12% ~03s
|+++++++ | 13% ~03s
|++++++++ | 14% ~03s
|++++++++ | 16% ~03s
|+++++++++ | 17% ~03s
|++++++++++ | 18% ~03s
|++++++++++ | 20% ~03s
|+++++++++++ | 21% ~03s
|++++++++++++ | 22% ~03s
|++++++++++++ | 24% ~03s
|+++++++++++++ | 25% ~03s
|++++++++++++++ | 26% ~03s
|++++++++++++++ | 28% ~03s
|+++++++++++++++ | 29% ~03s
|++++++++++++++++ | 30% ~03s
|++++++++++++++++ | 32% ~03s
|+++++++++++++++++ | 33% ~02s
|++++++++++++++++++ | 34% ~02s
|++++++++++++++++++ | 36% ~02s
|+++++++++++++++++++ | 37% ~02s
|++++++++++++++++++++ | 38% ~02s
|++++++++++++++++++++ | 39% ~02s
|+++++++++++++++++++++ | 41% ~02s
|++++++++++++++++++++++ | 42% ~02s
|++++++++++++++++++++++ | 43% ~02s
|+++++++++++++++++++++++ | 45% ~02s
|++++++++++++++++++++++++ | 46% ~02s
|++++++++++++++++++++++++ | 47% ~02s
|+++++++++++++++++++++++++ | 49% ~02s
|+++++++++++++++++++++++++ | 50% ~02s
|++++++++++++++++++++++++++ | 51% ~02s
|+++++++++++++++++++++++++++ | 53% ~02s
|+++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 55% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|+++++++++++++++++++++++++++++ | 58% ~02s
|++++++++++++++++++++++++++++++ | 59% ~01s
|+++++++++++++++++++++++++++++++ | 61% ~01s
|+++++++++++++++++++++++++++++++ | 62% ~01s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|+++++++++++++++++++++++++++++++++ | 64% ~01s
|+++++++++++++++++++++++++++++++++ | 66% ~01s
|++++++++++++++++++++++++++++++++++ | 67% ~01s
|+++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 71% ~01s
|+++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s Calculating cluster 5
| | 0 % ~calculating
|+ | 1 % ~09s
|++ | 2 % ~09s
|++ | 3 % ~09s
|+++ | 4 % ~09s
|+++ | 5 % ~09s
|++++ | 7 % ~09s
|++++ | 8 % ~09s
|+++++ | 9 % ~09s
|+++++ | 10% ~09s
|++++++ | 11% ~09s
|+++++++ | 12% ~09s
|+++++++ | 13% ~09s
|++++++++ | 14% ~08s
|++++++++ | 15% ~08s
|+++++++++ | 16% ~08s
|+++++++++ | 18% ~08s
|++++++++++ | 19% ~08s
|++++++++++ | 20% ~08s
|+++++++++++ | 21% ~08s
|+++++++++++ | 22% ~08s
|++++++++++++ | 23% ~08s
|+++++++++++++ | 24% ~07s
|+++++++++++++ | 25% ~07s
|++++++++++++++ | 26% ~07s
|++++++++++++++ | 27% ~07s
|+++++++++++++++ | 29% ~07s
|+++++++++++++++ | 30% ~07s
|++++++++++++++++ | 31% ~07s
|++++++++++++++++ | 32% ~07s
|+++++++++++++++++ | 33% ~07s
|++++++++++++++++++ | 34% ~06s
|++++++++++++++++++ | 35% ~06s
|+++++++++++++++++++ | 36% ~06s
|+++++++++++++++++++ | 37% ~06s
|++++++++++++++++++++ | 38% ~06s
|++++++++++++++++++++ | 40% ~06s
|+++++++++++++++++++++ | 41% ~06s
|+++++++++++++++++++++ | 42% ~06s
|++++++++++++++++++++++ | 43% ~06s
|++++++++++++++++++++++ | 44% ~06s
|+++++++++++++++++++++++ | 45% ~05s
|++++++++++++++++++++++++ | 46% ~05s
|++++++++++++++++++++++++ | 47% ~05s
|+++++++++++++++++++++++++ | 48% ~05s
|+++++++++++++++++++++++++ | 49% ~05s
|++++++++++++++++++++++++++ | 51% ~05s
|++++++++++++++++++++++++++ | 52% ~05s
|+++++++++++++++++++++++++++ | 53% ~05s
|+++++++++++++++++++++++++++ | 54% ~05s
|++++++++++++++++++++++++++++ | 55% ~04s
|+++++++++++++++++++++++++++++ | 56% ~04s
|+++++++++++++++++++++++++++++ | 57% ~04s
|++++++++++++++++++++++++++++++ | 58% ~04s
|++++++++++++++++++++++++++++++ | 59% ~04s
|+++++++++++++++++++++++++++++++ | 60% ~04s
|+++++++++++++++++++++++++++++++ | 62% ~04s
|++++++++++++++++++++++++++++++++ | 63% ~04s
|++++++++++++++++++++++++++++++++ | 64% ~04s
|+++++++++++++++++++++++++++++++++ | 65% ~03s
|+++++++++++++++++++++++++++++++++ | 66% ~03s
|++++++++++++++++++++++++++++++++++ | 67% ~03s
|+++++++++++++++++++++++++++++++++++ | 68% ~03s
|+++++++++++++++++++++++++++++++++++ | 69% ~03s
|++++++++++++++++++++++++++++++++++++ | 70% ~03s
|++++++++++++++++++++++++++++++++++++ | 71% ~03s
|+++++++++++++++++++++++++++++++++++++ | 73% ~03s
|+++++++++++++++++++++++++++++++++++++ | 74% ~03s
|++++++++++++++++++++++++++++++++++++++ | 75% ~03s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=10s Calculating cluster 6
| | 0 % ~calculating
|+ | 1 % ~07s
|++ | 2 % ~07s
|++ | 4 % ~06s
|+++ | 5 % ~06s
|+++ | 6 % ~06s
|++++ | 7 % ~06s
|+++++ | 8 % ~06s
|+++++ | 9 % ~06s
|++++++ | 11% ~06s
|++++++ | 12% ~06s
|+++++++ | 13% ~06s
|++++++++ | 14% ~06s
|++++++++ | 15% ~06s
|+++++++++ | 16% ~05s
|+++++++++ | 18% ~05s
|++++++++++ | 19% ~05s
|++++++++++ | 20% ~05s
|+++++++++++ | 21% ~05s
|++++++++++++ | 22% ~05s
|++++++++++++ | 24% ~05s
|+++++++++++++ | 25% ~05s
|+++++++++++++ | 26% ~05s
|++++++++++++++ | 27% ~05s
|+++++++++++++++ | 28% ~05s
|+++++++++++++++ | 29% ~05s
|++++++++++++++++ | 31% ~05s
|++++++++++++++++ | 32% ~05s
|+++++++++++++++++ | 33% ~04s
|++++++++++++++++++ | 34% ~04s
|++++++++++++++++++ | 35% ~04s
|+++++++++++++++++++ | 36% ~04s
|+++++++++++++++++++ | 38% ~04s
|++++++++++++++++++++ | 39% ~04s
|++++++++++++++++++++ | 40% ~04s
|+++++++++++++++++++++ | 41% ~04s
|++++++++++++++++++++++ | 42% ~04s
|++++++++++++++++++++++ | 44% ~04s
|+++++++++++++++++++++++ | 45% ~04s
|+++++++++++++++++++++++ | 46% ~04s
|++++++++++++++++++++++++ | 47% ~04s
|+++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 53% ~03s
|++++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~03s
|+++++++++++++++++++++++++++++ | 56% ~03s
|+++++++++++++++++++++++++++++ | 58% ~03s
|++++++++++++++++++++++++++++++ | 59% ~03s
|++++++++++++++++++++++++++++++ | 60% ~03s
|+++++++++++++++++++++++++++++++ | 61% ~03s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|+++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~02s
|++++++++++++++++++++++++++++++++++++++ | 74% ~02s
|++++++++++++++++++++++++++++++++++++++ | 75% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=07s Calculating cluster 7
| | 0 % ~calculating
|+ | 1 % ~05s
|++ | 2 % ~05s
|++ | 4 % ~05s
|+++ | 5 % ~05s
|++++ | 6 % ~05s
|++++ | 7 % ~05s
|+++++ | 9 % ~05s
|+++++ | 10% ~05s
|++++++ | 11% ~05s
|+++++++ | 12% ~05s
|+++++++ | 13% ~05s
|++++++++ | 15% ~05s
|++++++++ | 16% ~04s
|+++++++++ | 17% ~04s
|++++++++++ | 18% ~04s
|++++++++++ | 20% ~04s
|+++++++++++ | 21% ~04s
|+++++++++++ | 22% ~04s
|++++++++++++ | 23% ~04s
|+++++++++++++ | 24% ~04s
|+++++++++++++ | 26% ~04s
|++++++++++++++ | 27% ~04s
|+++++++++++++++ | 28% ~04s
|+++++++++++++++ | 29% ~04s
|++++++++++++++++ | 30% ~04s
|++++++++++++++++ | 32% ~04s
|+++++++++++++++++ | 33% ~04s
|++++++++++++++++++ | 34% ~04s
|++++++++++++++++++ | 35% ~04s
|+++++++++++++++++++ | 37% ~03s
|+++++++++++++++++++ | 38% ~03s
|++++++++++++++++++++ | 39% ~03s
|+++++++++++++++++++++ | 40% ~03s
|+++++++++++++++++++++ | 41% ~03s
|++++++++++++++++++++++ | 43% ~03s
|++++++++++++++++++++++ | 44% ~03s
|+++++++++++++++++++++++ | 45% ~03s
|++++++++++++++++++++++++ | 46% ~03s
|++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|+++++++++++++++++++++++++ | 50% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|+++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 54% ~03s
|++++++++++++++++++++++++++++ | 55% ~02s
|+++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 61% ~02s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~02s
|+++++++++++++++++++++++++++++++++ | 65% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|+++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|++++++++++++++++++++++++++++++++++++ | 72% ~02s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|++++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05s Calculating cluster 8
| | 0 % ~calculating
|+ | 1 % ~04s
|++ | 2 % ~04s
|++ | 3 % ~04s
|+++ | 4 % ~04s
|+++ | 5 % ~04s
|++++ | 6 % ~04s
|++++ | 7 % ~04s
|+++++ | 8 % ~04s
|+++++ | 9 % ~04s
|++++++ | 10% ~04s
|++++++ | 11% ~04s
|+++++++ | 12% ~04s
|+++++++ | 13% ~04s
|++++++++ | 14% ~04s
|++++++++ | 15% ~04s
|+++++++++ | 16% ~04s
|+++++++++ | 17% ~03s
|++++++++++ | 18% ~03s
|++++++++++ | 19% ~03s
|+++++++++++ | 20% ~03s
|+++++++++++ | 21% ~03s
|++++++++++++ | 22% ~03s
|++++++++++++ | 23% ~03s
|+++++++++++++ | 24% ~03s
|+++++++++++++ | 26% ~03s
|++++++++++++++ | 27% ~03s
|++++++++++++++ | 28% ~03s
|+++++++++++++++ | 29% ~03s
|+++++++++++++++ | 30% ~03s
|++++++++++++++++ | 31% ~03s
|++++++++++++++++ | 32% ~03s
|+++++++++++++++++ | 33% ~03s
|+++++++++++++++++ | 34% ~03s
|++++++++++++++++++ | 35% ~03s
|++++++++++++++++++ | 36% ~03s
|+++++++++++++++++++ | 37% ~03s
|+++++++++++++++++++ | 38% ~03s
|++++++++++++++++++++ | 39% ~02s
|++++++++++++++++++++ | 40% ~02s
|+++++++++++++++++++++ | 41% ~02s
|+++++++++++++++++++++ | 42% ~02s
|++++++++++++++++++++++ | 43% ~02s
|++++++++++++++++++++++ | 44% ~02s
|+++++++++++++++++++++++ | 45% ~02s
|+++++++++++++++++++++++ | 46% ~02s
|++++++++++++++++++++++++ | 47% ~02s
|++++++++++++++++++++++++ | 48% ~02s
|+++++++++++++++++++++++++ | 49% ~02s
|+++++++++++++++++++++++++ | 50% ~02s
|++++++++++++++++++++++++++ | 51% ~02s
|+++++++++++++++++++++++++++ | 52% ~02s
|+++++++++++++++++++++++++++ | 53% ~02s
|++++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 55% ~02s
|+++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|++++++++++++++++++++++++++++++ | 58% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|+++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 61% ~02s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|+++++++++++++++++++++++++++++++++ | 64% ~01s
|+++++++++++++++++++++++++++++++++ | 65% ~01s
|++++++++++++++++++++++++++++++++++ | 66% ~01s
|++++++++++++++++++++++++++++++++++ | 67% ~01s
|+++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 69% ~01s
|++++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 71% ~01s
|+++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|++++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s Calculating cluster 9
| | 0 % ~calculating
|+ | 1 % ~05s
|++ | 2 % ~05s
|++ | 3 % ~05s
|+++ | 5 % ~05s
|+++ | 6 % ~05s
|++++ | 7 % ~05s
|+++++ | 8 % ~05s
|+++++ | 9 % ~05s
|++++++ | 10% ~05s
|++++++ | 11% ~05s
|+++++++ | 13% ~05s
|+++++++ | 14% ~04s
|++++++++ | 15% ~04s
|+++++++++ | 16% ~04s
|+++++++++ | 17% ~04s
|++++++++++ | 18% ~04s
|++++++++++ | 20% ~04s
|+++++++++++ | 21% ~04s
|+++++++++++ | 22% ~04s
|++++++++++++ | 23% ~04s
|+++++++++++++ | 24% ~04s
|+++++++++++++ | 25% ~04s
|++++++++++++++ | 26% ~04s
|++++++++++++++ | 28% ~04s
|+++++++++++++++ | 29% ~04s
|+++++++++++++++ | 30% ~04s
|++++++++++++++++ | 31% ~04s
|+++++++++++++++++ | 32% ~04s
|+++++++++++++++++ | 33% ~03s
|++++++++++++++++++ | 34% ~03s
|++++++++++++++++++ | 36% ~03s
|+++++++++++++++++++ | 37% ~03s
|+++++++++++++++++++ | 38% ~03s
|++++++++++++++++++++ | 39% ~03s
|+++++++++++++++++++++ | 40% ~03s
|+++++++++++++++++++++ | 41% ~03s
|++++++++++++++++++++++ | 43% ~03s
|++++++++++++++++++++++ | 44% ~03s
|+++++++++++++++++++++++ | 45% ~03s
|+++++++++++++++++++++++ | 46% ~03s
|++++++++++++++++++++++++ | 47% ~03s
|+++++++++++++++++++++++++ | 48% ~03s
|+++++++++++++++++++++++++ | 49% ~03s
|++++++++++++++++++++++++++ | 51% ~03s
|++++++++++++++++++++++++++ | 52% ~03s
|+++++++++++++++++++++++++++ | 53% ~02s
|++++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 55% ~02s
|+++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 61% ~02s
|++++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~02s
|+++++++++++++++++++++++++++++++++ | 64% ~02s
|+++++++++++++++++++++++++++++++++ | 66% ~02s
|++++++++++++++++++++++++++++++++++ | 67% ~02s
|++++++++++++++++++++++++++++++++++ | 68% ~02s
|+++++++++++++++++++++++++++++++++++ | 69% ~02s
|++++++++++++++++++++++++++++++++++++ | 70% ~02s
|++++++++++++++++++++++++++++++++++++ | 71% ~02s
|+++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05s Calculating cluster 10
| | 0 % ~calculating
|+ | 1 % ~03s
|++ | 3 % ~03s
|+++ | 4 % ~02s
|+++ | 6 % ~02s
|++++ | 7 % ~02s
|+++++ | 8 % ~02s
|+++++ | 10% ~02s
|++++++ | 11% ~02s
|+++++++ | 13% ~02s
|++++++++ | 14% ~02s
|++++++++ | 15% ~02s
|+++++++++ | 17% ~02s
|++++++++++ | 18% ~02s
|++++++++++ | 20% ~02s
|+++++++++++ | 21% ~02s
|++++++++++++ | 23% ~02s
|++++++++++++ | 24% ~02s
|+++++++++++++ | 25% ~02s
|++++++++++++++ | 27% ~02s
|+++++++++++++++ | 28% ~02s
|+++++++++++++++ | 30% ~02s
|++++++++++++++++ | 31% ~02s
|+++++++++++++++++ | 32% ~02s
|+++++++++++++++++ | 34% ~02s
|++++++++++++++++++ | 35% ~02s
|+++++++++++++++++++ | 37% ~02s
|++++++++++++++++++++ | 38% ~02s
|++++++++++++++++++++ | 39% ~02s
|+++++++++++++++++++++ | 41% ~02s
|++++++++++++++++++++++ | 42% ~01s
|++++++++++++++++++++++ | 44% ~01s
|+++++++++++++++++++++++ | 45% ~01s
|++++++++++++++++++++++++ | 46% ~01s
|++++++++++++++++++++++++ | 48% ~01s
|+++++++++++++++++++++++++ | 49% ~01s
|++++++++++++++++++++++++++ | 51% ~01s
|+++++++++++++++++++++++++++ | 52% ~01s
|+++++++++++++++++++++++++++ | 54% ~01s
|++++++++++++++++++++++++++++ | 55% ~01s
|+++++++++++++++++++++++++++++ | 56% ~01s
|+++++++++++++++++++++++++++++ | 58% ~01s
|++++++++++++++++++++++++++++++ | 59% ~01s
|+++++++++++++++++++++++++++++++ | 61% ~01s
|+++++++++++++++++++++++++++++++ | 62% ~01s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|+++++++++++++++++++++++++++++++++ | 65% ~01s
|++++++++++++++++++++++++++++++++++ | 66% ~01s
|++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 69% ~01s
|++++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~00s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~00s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~00s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~00s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=03s Calculating cluster 11
| | 0 % ~calculating
|+ | 1 % ~04s
|++ | 2 % ~04s
|++ | 4 % ~04s
|+++ | 5 % ~04s
|++++ | 6 % ~04s
|++++ | 7 % ~04s
|+++++ | 9 % ~04s
|+++++ | 10% ~04s
|++++++ | 11% ~04s
|+++++++ | 12% ~03s
|+++++++ | 14% ~03s
|++++++++ | 15% ~03s
|+++++++++ | 16% ~03s
|+++++++++ | 17% ~03s
|++++++++++ | 19% ~03s
|++++++++++ | 20% ~03s
|+++++++++++ | 21% ~03s
|++++++++++++ | 22% ~03s
|++++++++++++ | 23% ~03s
|+++++++++++++ | 25% ~03s
|+++++++++++++ | 26% ~03s
|++++++++++++++ | 27% ~03s
|+++++++++++++++ | 28% ~03s
|+++++++++++++++ | 30% ~03s
|++++++++++++++++ | 31% ~03s
|+++++++++++++++++ | 32% ~03s
|+++++++++++++++++ | 33% ~03s
|++++++++++++++++++ | 35% ~03s
|++++++++++++++++++ | 36% ~03s
|+++++++++++++++++++ | 37% ~02s
|++++++++++++++++++++ | 38% ~02s
|++++++++++++++++++++ | 40% ~02s
|+++++++++++++++++++++ | 41% ~02s
|+++++++++++++++++++++ | 42% ~02s
|++++++++++++++++++++++ | 43% ~02s
|+++++++++++++++++++++++ | 44% ~02s
|+++++++++++++++++++++++ | 46% ~02s
|++++++++++++++++++++++++ | 47% ~02s
|+++++++++++++++++++++++++ | 48% ~02s
|+++++++++++++++++++++++++ | 49% ~02s
|++++++++++++++++++++++++++ | 51% ~02s
|++++++++++++++++++++++++++ | 52% ~02s
|+++++++++++++++++++++++++++ | 53% ~02s
|++++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|++++++++++++++++++++++++++++++ | 58% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|+++++++++++++++++++++++++++++++ | 60% ~02s
|+++++++++++++++++++++++++++++++ | 62% ~02s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|+++++++++++++++++++++++++++++++++ | 64% ~01s
|+++++++++++++++++++++++++++++++++ | 65% ~01s
|++++++++++++++++++++++++++++++++++ | 67% ~01s
|++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 69% ~01s
|++++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|++++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s Calculating cluster 12
| | 0 % ~calculating
|+ | 1 % ~10s
|++ | 2 % ~10s
|++ | 3 % ~09s
|+++ | 4 % ~09s
|+++ | 6 % ~09s
|++++ | 7 % ~09s
|++++ | 8 % ~09s
|+++++ | 9 % ~09s
|+++++ | 10% ~09s
|++++++ | 11% ~09s
|+++++++ | 12% ~09s
|+++++++ | 13% ~08s
|++++++++ | 14% ~08s
|++++++++ | 16% ~08s
|+++++++++ | 17% ~08s
|+++++++++ | 18% ~08s
|++++++++++ | 19% ~08s
|++++++++++ | 20% ~08s
|+++++++++++ | 21% ~08s
|++++++++++++ | 22% ~08s
|++++++++++++ | 23% ~07s
|+++++++++++++ | 24% ~07s
|+++++++++++++ | 26% ~07s
|++++++++++++++ | 27% ~07s
|++++++++++++++ | 28% ~07s
|+++++++++++++++ | 29% ~07s
|+++++++++++++++ | 30% ~07s
|++++++++++++++++ | 31% ~07s
|+++++++++++++++++ | 32% ~07s
|+++++++++++++++++ | 33% ~07s
|++++++++++++++++++ | 34% ~06s
|++++++++++++++++++ | 36% ~06s
|+++++++++++++++++++ | 37% ~06s
|+++++++++++++++++++ | 38% ~06s
|++++++++++++++++++++ | 39% ~06s
|++++++++++++++++++++ | 40% ~06s
|+++++++++++++++++++++ | 41% ~06s
|++++++++++++++++++++++ | 42% ~06s
|++++++++++++++++++++++ | 43% ~06s
|+++++++++++++++++++++++ | 44% ~05s
|+++++++++++++++++++++++ | 46% ~05s
|++++++++++++++++++++++++ | 47% ~05s
|++++++++++++++++++++++++ | 48% ~05s
|+++++++++++++++++++++++++ | 49% ~05s
|+++++++++++++++++++++++++ | 50% ~05s
|++++++++++++++++++++++++++ | 51% ~05s
|+++++++++++++++++++++++++++ | 52% ~05s
|+++++++++++++++++++++++++++ | 53% ~05s
|++++++++++++++++++++++++++++ | 54% ~04s
|++++++++++++++++++++++++++++ | 56% ~04s
|+++++++++++++++++++++++++++++ | 57% ~04s
|+++++++++++++++++++++++++++++ | 58% ~04s
|++++++++++++++++++++++++++++++ | 59% ~04s
|++++++++++++++++++++++++++++++ | 60% ~04s
|+++++++++++++++++++++++++++++++ | 61% ~04s
|++++++++++++++++++++++++++++++++ | 62% ~04s
|++++++++++++++++++++++++++++++++ | 63% ~04s
|+++++++++++++++++++++++++++++++++ | 64% ~03s
|+++++++++++++++++++++++++++++++++ | 66% ~03s
|++++++++++++++++++++++++++++++++++ | 67% ~03s
|++++++++++++++++++++++++++++++++++ | 68% ~03s
|+++++++++++++++++++++++++++++++++++ | 69% ~03s
|+++++++++++++++++++++++++++++++++++ | 70% ~03s
|++++++++++++++++++++++++++++++++++++ | 71% ~03s
|+++++++++++++++++++++++++++++++++++++ | 72% ~03s
|+++++++++++++++++++++++++++++++++++++ | 73% ~03s
|++++++++++++++++++++++++++++++++++++++ | 74% ~03s
|++++++++++++++++++++++++++++++++++++++ | 76% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~02s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~02s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~02s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=10s Calculating cluster 13
| | 0 % ~calculating
|+ | 1 % ~04s
|++ | 2 % ~04s
|++ | 3 % ~04s
|+++ | 4 % ~04s
|+++ | 5 % ~04s
|++++ | 6 % ~03s
|++++ | 7 % ~03s
|+++++ | 8 % ~03s
|+++++ | 9 % ~03s
|++++++ | 10% ~03s
|++++++ | 11% ~03s
|+++++++ | 12% ~03s
|+++++++ | 13% ~03s
|++++++++ | 14% ~03s
|++++++++ | 15% ~03s
|+++++++++ | 16% ~03s
|+++++++++ | 17% ~03s
|++++++++++ | 18% ~03s
|++++++++++ | 19% ~03s
|+++++++++++ | 20% ~03s
|+++++++++++ | 21% ~03s
|++++++++++++ | 22% ~03s
|++++++++++++ | 23% ~03s
|+++++++++++++ | 24% ~03s
|+++++++++++++ | 25% ~03s
|++++++++++++++ | 26% ~03s
|++++++++++++++ | 27% ~03s
|+++++++++++++++ | 28% ~03s
|+++++++++++++++ | 29% ~03s
|++++++++++++++++ | 30% ~03s
|++++++++++++++++ | 31% ~03s
|+++++++++++++++++ | 32% ~02s
|+++++++++++++++++ | 33% ~02s
|++++++++++++++++++ | 34% ~02s
|++++++++++++++++++ | 35% ~02s
|+++++++++++++++++++ | 36% ~02s
|+++++++++++++++++++ | 37% ~02s
|++++++++++++++++++++ | 38% ~02s
|++++++++++++++++++++ | 39% ~02s
|+++++++++++++++++++++ | 40% ~02s
|+++++++++++++++++++++ | 41% ~02s
|++++++++++++++++++++++ | 42% ~02s
|++++++++++++++++++++++ | 43% ~02s
|+++++++++++++++++++++++ | 44% ~02s
|+++++++++++++++++++++++ | 45% ~02s
|++++++++++++++++++++++++ | 46% ~02s
|++++++++++++++++++++++++ | 47% ~02s
|+++++++++++++++++++++++++ | 48% ~02s
|+++++++++++++++++++++++++ | 49% ~02s
|++++++++++++++++++++++++++ | 51% ~02s
|++++++++++++++++++++++++++ | 52% ~02s
|+++++++++++++++++++++++++++ | 53% ~02s
|+++++++++++++++++++++++++++ | 54% ~02s
|++++++++++++++++++++++++++++ | 55% ~02s
|++++++++++++++++++++++++++++ | 56% ~02s
|+++++++++++++++++++++++++++++ | 57% ~02s
|+++++++++++++++++++++++++++++ | 58% ~02s
|++++++++++++++++++++++++++++++ | 59% ~02s
|++++++++++++++++++++++++++++++ | 60% ~01s
|+++++++++++++++++++++++++++++++ | 61% ~01s
|+++++++++++++++++++++++++++++++ | 62% ~01s
|++++++++++++++++++++++++++++++++ | 63% ~01s
|++++++++++++++++++++++++++++++++ | 64% ~01s
|+++++++++++++++++++++++++++++++++ | 65% ~01s
|+++++++++++++++++++++++++++++++++ | 66% ~01s
|++++++++++++++++++++++++++++++++++ | 67% ~01s
|++++++++++++++++++++++++++++++++++ | 68% ~01s
|+++++++++++++++++++++++++++++++++++ | 69% ~01s
|+++++++++++++++++++++++++++++++++++ | 70% ~01s
|++++++++++++++++++++++++++++++++++++ | 71% ~01s
|++++++++++++++++++++++++++++++++++++ | 72% ~01s
|+++++++++++++++++++++++++++++++++++++ | 73% ~01s
|+++++++++++++++++++++++++++++++++++++ | 74% ~01s
|++++++++++++++++++++++++++++++++++++++ | 75% ~01s
|++++++++++++++++++++++++++++++++++++++ | 76% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~01s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~01s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~01s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~01s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~01s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~01s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~00s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s top.markers <- all.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC)
top.markerswrite.table(all.markers,
file = "./figures/stimulation/downsampled_cluster_markers.tsv",
sep = "\t",
quote = FALSE,
row.names = FALSE)Calculate DE genes: for each cluster, compare stim VS unstim
for (clust in levels(as.factor(Idents(scSeurat)))) {
cells_stim <- colnames(scSeurat)[Idents(scSeurat) == clust & scSeurat$tissue_type == "6hrs_PMAIO"]
cells_unstim <- colnames(scSeurat)[Idents(scSeurat) == clust & scSeurat$tissue_type == "6hrs_unstim"]
markers <- RunPresto(scSeurat,
ident.1 = cells_stim,
ident.2 = cells_unstim,
only.pos = FALSE,
min.pct = 0.25,
logfc.threshold = 0.25,
recorrect_umi = FALSE)
write.table(markers,
file = paste("./figures/stimulation/downsampled_markers_cluster",
clust ,"_stim_vs_unstim.tsv", sep = ""),
sep = "\t",
quote = FALSE,
row.names = FALSE)
}Look for T-cell signatures.
FeaturePlot(scSeurat, features = c("CD3E", "NKG7"))
FeaturePlot(scSeurat, features = c("LEF1", "XCL1;XCL2"))
FeaturePlot(scSeurat, features = c("TOX", "CD8A"))
FeaturePlot(scSeurat, features = c("CCR7"))
Look for macrophage signatures:
FeaturePlot(scSeurat, features = c("LGALS1", "TYROBP"))
FeaturePlot(scSeurat, features = c("MARCO", "C1QC"))
FeaturePlot(scSeurat, features = c("LYZ-1", "S100A8"))
FeaturePlot(scSeurat, features = c("DEFA6;DEFA4;DEFA5", "CTSS"))
FeaturePlot(scSeurat, features = c("FLT3", "S100A12"))
Look for B and plasma cell signatures
FeaturePlot(scSeurat, features = c("CD79B", "JCHAIN"))
Cluster 12 is the only cluster that is obviously dominated by the unstimulated experiments. What cells are these? Looks like they are hepatocytes. A lot of the markers are periportal, but all hepatocytes are in this cluster.
# Isolate DE genes
clust11 <- sCVdata_list$res.0.4@DEvsRest$`12`[order(sCVdata_list$res.0.4@DEvsRest$`12`$Wstat,
decreasing = TRUE), ]
rownames(clust11)[1:50] [1] "PAH" "LOC114082496" "TDO2" "MAT1A" "GYS2"
[6] "SLCO1B3;SLCO1B3-SLCO1B7;SLCO1B7;SLCO1B1" "FBP1" "CPS1" "SLC2A2" "ALDOB"
[11] "MTSS1" "IGFBP1" "CYP3A4;CYP3A7-CYP3A51P;CYP3A7-2" "mikado.WCK01-AAH20201022-F8-rsc00143G668" "PCK1"
[16] "SHMT1" "CYP3A4;CYP3A7-CYP3A51P;CYP3A7" "ARG1" "CYP3A4;CYP3A7-CYP3A51P;CYP3A7-3" "LOC107139912"
[21] "ALB-1" "SLC38A4" "LOC107139914" "SORBS2" "TAT"
[26] "C5-1" "KLKB1" "Slc22a19-1" "G6PC1" "RBP4"
[31] "AGMO" "HSD17B11" "CMBL" "SLC25A13" "ZBTB16"
[36] "C8G" "PYGL" "HSD11B1" "mikado.WCK01-AAH20201022-F8-rsc00060G101" "CES3"
[41] "MTARC2" "IDO2" "AQP9" "ACACB" "GOT1"
[46] "CFI" "NR1I2" "ABCB11" "SOX5" "BHMT2" FeaturePlot(scSeurat, features = c("PAH","PCK1"))
FeaturePlot(scSeurat, features = c("CYP2E1","FETUB"))
FeaturePlot(scSeurat, features = c("ACACB","ELOVL6"))
FeaturePlot(scSeurat, features = c("POLR2D", "ALB-1"))
Let’s look at some of the key markers that Sonya sent: IL2, IL4, IL6, IL7, IL10, IL12A, TGFB
FeaturePlot(scSeurat, features = c("IL2", "IL4"))
FeaturePlot(scSeurat, features = c("IL6", "IL6-1"))
FeaturePlot(scSeurat, features = c("IL7", "IL10"))
FeaturePlot(scSeurat, features = c("IL12A", "TGFB1"))
It’s pretty hard to see which cytokines are expressed in which samples, so I’m going to try splitting up the samples.
DimPlot(scSeurat, split.by = "tissue_type", label = TRUE) & NoLegend()
pdf(file = './figures/stimulation/downsampled_UMAP_split.pdf')DimPlot(scSeurat, split.by = "tissue_type", label = TRUE) & NoLegend()
dev.off()png
2
Now let’s take a look at the features on this split plot.
genes <- c("IL2","IL4","IL6","IL7","IL10","IL12A","TGFB1","TGFB2","TGFB3","TNF","IL18","IL2RA","CCL5","IFNG","LIF", "CCL3L1;CCL3L3;CCL3;CCL18","CCL4L2;CCL4L1;CCL4")
for (gene in genes) {
print(FeaturePlot(scSeurat, feature = gene, split.by = "tissue_type"))
pdf(paste("figures/stimulation/downsampled_UMAP_split_", gene, ".pdf", sep = ""))
print(FeaturePlot(scSeurat, feature = gene, split.by = "tissue_type"))
dev.off()
}Warning: All cells have the same value (0) of “IL2”More plots
Cluster 2 looks like it generally has more IL genes expressed. Isolate DE genes for this cluster.
clust1 <- sCVdata_list$res.0.4@DEvsRest$`2`[order(sCVdata_list$res.0.4@DEvsRest$`2`$Wstat,
decreasing = TRUE), ]
cat(rownames(clust1)[1:50])PTPRC TOX PRKCH INPP4B mikado.WCK01-AAH20201022-F8-rsc00190G443 ARID5B IKZF3 ARHGAP15 SATB1 DOCK10 TRPS1 RASA2 SAMSN1 NSD3 MBNL1 SH3KBP1 EMB SYTL3 ICOS mikado.WCK01-AAH20201022-F8-rsc00083G981 mikado.WCK01-AAH20201022-F8-rsc00275G164 THEMIS MSI2 SLAMF1 PITPNC1 NXF2;NXF2B;NXF5 SRSF7 IKZF1 RAPGEF6 STAT4 SLC38A1 RAP1A RABGAP1L ZC3HAV1 BCL2 TESPA1 APBB1IP GIMAP7 DHX8 DDX5 UBAC2 HUWE1 CD3E CTLA4 CD44 GIMAP1 RGS1 MTHFD1L RIPOR2 TANKVisualise these genes in violin plots.
Interpretation: Now I see that IL2 and IL4 are expressed in more than just cluster 2, but it is nearly always in PMAIO. Cluster 8 is definitely where IL6 is expressed. IL7 is a bit more spread out across treatment types, but it’s definitely present in PMAIO in clusters 4, 5, and 11. Cluster 11 is plasma cells, but I’m honestly not sure of 4 and 5 - low signal hepatocytes? IL10 is in clusters 2 and 11 PMAIO. IL12A is a bit more in 4 and 5 PMAIO.
VlnPlot(scSeurat, feature = "IL2", split.by = "tissue_type") # Only in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL4", split.by = "tissue_type") # Only in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL6", split.by = "tissue_type") # Stronger in endo and mesem PMAIO
VlnPlot(scSeurat, feature = "IL6-1", split.by = "tissue_type") # No signal
VlnPlot(scSeurat, feature = "IL7", split.by = "tissue_type") # More in PMAIO cluster 4/5
VlnPlot(scSeurat, feature = "IL10", split.by = "tissue_type") # More in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL12A", split.by = "tissue_type") # A bit more in 1,4,5
VlnPlot(scSeurat, feature = "TGFB1", split.by = "tissue_type") # Pretty even across all
VlnPlot(scSeurat, feature = "TNF", split.by = "tissue_type")
Make Violin plots with ggplot
genes <- c("IL2","IL4","IL6","IL7","IL10","IL12A","TGFB1","TGFB2","TGFB3","TNF","IL18","IL2RA","CCL5","IFNG","LIF")
for(gene in genes) {
vln_df = data.frame(gene = scSeurat[["RNA"]]@data[gene,],
Cluster = Idents(scSeurat),
tissue_type = scSeurat$tissue_type)
plot <- ggplot(vln_df, aes(x = Cluster, y = gene)) +
geom_violin(aes(fill = tissue_type), trim=TRUE, scale = "width") +
ylab(gene) +
theme_bw()
print(plot)
pdf(file = paste("figures/stimulation/downsampled_vlnPlot_split_", gene, ".pdf", sep = ""))
print(plot) # Need print function because R doesn't autoprint in loops
dev.off()
}
Looking for more genes
gene <- "IL18"
vln_df = data.frame(gene = scSeurat[["RNA"]]@data[gene,],
Cluster = Idents(scSeurat),
tissue_type = scSeurat$tissue_type)
plot <- ggplot(vln_df, aes(x = Cluster, y = gene)) +
geom_violin(aes(fill = tissue_type), trim=TRUE, scale = "width") +
ylab(gene) +
theme_bw()
print(plot)
Perform DE test on T-cells from PMAIO vs unstim T-cells. I see TNF, IL2RA, but I also see hepatocyte genes like ALB-1, STAT3
cat(row.names(de_results)[1:100], sep = " ")
LOC107134468 CCL4L2;CCL4L1;CCL4 mikado.WCK01-AAH20201022-F8-rsc00073G191 MTHFD1L NFKB1 NXF2;NXF2B;NXF5 CCND3 IFNG SATB1 SKAP1 ARID5B mikado.WCK01-AAH20201022-F8-rsc00334G1 CCL3L1;CCL3L3;CCL3;CCL18 SLAMF1 CD200 GIMAP7 LOC114086011-6 GBP7;GBP4 CBLB TRAF3IP3 NR4A3 ALB-1 TNFRSF9 SLC25A26 SYNE1 STAT3 UTRN HUWE1 PDE7A IL2RA PTPRCAP APOA1 TNRC6B Ifi214;Ifi209 ETS1 ANKRD44 MAPK6 PDE3B RESF1 CD27 mikado.WCK01-AAH20201022-F8-rsc00138G153 PICALM JARID2 MDN1 CHIC1 CCL3L1;CCL3L3;CCL3;CCL18-2 CKLF;CKLF-CMTM1 HECA FOXN3 MED13L SEC23B ZEB2 AMN1 CD3G SEC14L1 BATF LNPEP IRF4 ALB LOC107134769-1 IQGAP2 LOC114086011-12 SERPINA1 mikado.WCK01-AAH20201022-F8-rsc00234G885 TMEM156 STK4 ATP8A1 PECAM1 FAM13A MTHFD2 CELF2 SAMSN1 NUCB2 GIMAP1 SND1 VMP1 MLLT3 ASAP1 RBP4 TNF CRTAM FYN ACTB mikado.WCK01-AAH20201022-F8-rsc00190G443 PPP3CC HBS1L TTC27 B4GALT5 DDX5 ARHGDIB LAT CXCL2;CXCL3;CXCL1-1 ITM2B SENP7 DOCK8 RIPOR2 APBB1IP TRAF3 SAMHD1 ?}---
title: "Stimulation experiments"
output:
  html_document:
    df_print: paged
  html_notebook: default
  pdf_document: default
---

Analysis of stimulation experiments.

```{r}
library(Seurat)
library(dplyr)
library(ggplot2)
library(scClustViz)
library(SeuratWrappers)
```

Load integrated object. This object has been integrated with CCA, because there was lots of batch effect between the 0hr tissue and the other two experiments (which merged quite well).

```{r}
load("~/Dropbox/Zoe/scf_version/analysis/healthy_sc/seurat_objects/no_dropletQC/3391/integrated_3391_stimulation_pmaio_unstim_downsampled_cca_kanchor5_scClustViz.RData")
# Set identity
Idents(scSeurat) <- "integrated_snn_res.0.4"
```

Check out the UMAP of clusters, original identities, and refined SCINA labels.

```{r}
DimPlot(scSeurat, label = TRUE)
DimPlot(scSeurat, group.by = "tissue_type", label = FALSE)
DimPlot(scSeurat, group.by = "scina_labels", label = TRUE) & NoLegend()
```

```{r}
pdf(file = './figures/stimulation/downsampled_UMAP.pdf')
DimPlot(scSeurat, label = TRUE)
dev.off()
pdf(file = './figures/stimulation/downsampled_tissue_type_UMAP.pdf')
DimPlot(scSeurat, group.by = "tissue_type") +
  ggtitle(NULL)
dev.off()
```

Look at tissue-type per cluster on a proportional level:

```{r}
pt <- table(Idents(scSeurat), scSeurat$tissue_type)
pt <- as.data.frame(pt)
plot <- ggplot(pt, aes(x = Var1, y = Freq, fill = Var2)) +
  theme_bw(base_size = 15) +
  geom_col(position = "fill", width = 0.5) +
  xlab("Sample") +
  ylab("Proportion") +
  theme(legend.title = element_blank())
plot
pdf(file = './figures/stimulation/downsampled_tissue_type_barplot.pdf')
plot
dev.off()
```

Calculate all DE genes

```{r}
all.markers <- FindAllMarkers(scSeurat,
                              only.pos = TRUE,
                              min.pct = 0.25, 
                              logfc.threshold = 0.25,
                              recorrect_umi = FALSE)
top.markers <- all.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC)
top.markers
write.table(all.markers,
            file = "./figures/stimulation/downsampled_cluster_markers.tsv",
            sep = "\t",
            quote = FALSE,
            row.names = FALSE)
```

Calculate DE genes: for each cluster, compare stim VS unstim

```{r}
for (clust in levels(as.factor(Idents(scSeurat)))) {
  cells_stim <- colnames(scSeurat)[Idents(scSeurat) == clust & scSeurat$tissue_type == "6hrs_PMAIO"]
  cells_unstim <- colnames(scSeurat)[Idents(scSeurat) == clust & scSeurat$tissue_type == "6hrs_unstim"]
  markers <- RunPresto(scSeurat,
                       ident.1 = cells_stim,
                       ident.2 = cells_unstim,
                       only.pos = FALSE,
                       min.pct = 0.25,
                       logfc.threshold = 0.25,
                       recorrect_umi = FALSE)
  write.table(markers,
              file = paste("./figures/stimulation/downsampled_markers_cluster", 
                           clust ,"_stim_vs_unstim.tsv", sep = ""),
              sep = "\t",
              quote = FALSE,
              row.names = FALSE)
}
```

Look for T-cell signatures.

```{r}
FeaturePlot(scSeurat, features = c("CD3E", "NKG7"))
FeaturePlot(scSeurat, features = c("LEF1", "XCL1;XCL2"))
FeaturePlot(scSeurat, features = c("TOX", "CD8A"))
FeaturePlot(scSeurat, features = c("CCR7"))
```

Look for macrophage signatures:

```{r}
FeaturePlot(scSeurat, features = c("LGALS1", "TYROBP"))
FeaturePlot(scSeurat, features = c("MARCO", "C1QC"))
FeaturePlot(scSeurat, features = c("LYZ-1", "S100A8"))
FeaturePlot(scSeurat, features = c("DEFA6;DEFA4;DEFA5", "CTSS"))
FeaturePlot(scSeurat, features = c("FLT3", "S100A12"))
```

Look for B and plasma cell signatures

```{r}
FeaturePlot(scSeurat, features = c("CD79B", "JCHAIN"))
```


Cluster 12 is the only cluster that is obviously dominated by the unstimulated experiments. What cells are these? Looks like they are hepatocytes. A lot of the markers are periportal, but all hepatocytes are in this cluster.

```{r}
# Isolate DE genes
clust11 <- sCVdata_list$res.0.4@DEvsRest$`12`[order(sCVdata_list$res.0.4@DEvsRest$`12`$Wstat,
                                                    decreasing = TRUE), ]
rownames(clust11)[1:50]
FeaturePlot(scSeurat, features = c("PAH","PCK1"))
FeaturePlot(scSeurat, features = c("CYP2E1","FETUB"))
FeaturePlot(scSeurat, features = c("ACACB","ELOVL6"))
FeaturePlot(scSeurat, features = c("POLR2D", "ALB-1"))
```

Let's look at some of the key markers that Sonya sent: IL2, IL4, IL6, IL7, IL10, IL12A, TGFB

```{r}
FeaturePlot(scSeurat, features = c("IL2", "IL4"))
FeaturePlot(scSeurat, features = c("IL6", "IL6-1"))
FeaturePlot(scSeurat, features = c("IL7", "IL10"))
FeaturePlot(scSeurat, features = c("IL12A", "TGFB1"))
```

It's pretty hard to see which cytokines are expressed in which samples, so I'm going to try splitting up the samples.

```{r}
DimPlot(scSeurat, split.by = "tissue_type", label = TRUE) & NoLegend()
pdf(file = './figures/stimulation/downsampled_UMAP_split.pdf')
DimPlot(scSeurat, split.by = "tissue_type", label = TRUE) & NoLegend()
dev.off()
```

Now let's take a look at the features on this split plot.

```{r}
genes <- c("IL2","IL4","IL6","IL7","IL10","IL12A","TGFB1","TGFB2","TGFB3","TNF","IL18","IL2RA","CCL5","IFNG","LIF", "CCL3L1;CCL3L3;CCL3;CCL18","CCL4L2;CCL4L1;CCL4")
for (gene in genes) {
  print(FeaturePlot(scSeurat, feature = gene, split.by = "tissue_type"))
  pdf(paste("figures/stimulation/downsampled_UMAP_split_", gene, ".pdf", sep = ""))
  print(FeaturePlot(scSeurat, feature = gene, split.by = "tissue_type"))
  dev.off()
}
```

More plots

```{r}
FeaturePlot(scSeurat, feature = "IL15", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL16", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL17B", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL6ST", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL31RA", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL7R", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL7R-1", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL17D", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL5RA", split.by = "tissue_type") 
FeaturePlot(scSeurat, feature = "IL17RE", split.by = "tissue_type") 
FeaturePlot(scSeurat, feature = "IL17RC", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL17C", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL34", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL4I1", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL11", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL9R", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL4R", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL21R", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL27", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "ILK", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL18BP", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL10RA", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL3", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "CSF2", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IFNK", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL9", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL13", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "OSM", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "LIF", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "STAT1", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "STAT4", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL4", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL4I1", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "CD69", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "TLR7", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "HLA-DRA", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "IL12A", split.by = "tissue_type")
FeaturePlot(scSeurat, feature = "TLR2", split.by = "tissue_type")
```


Cluster 2 looks like it generally has more IL genes expressed. Isolate DE genes for this cluster.

```{r}
clust1 <- sCVdata_list$res.0.4@DEvsRest$`2`[order(sCVdata_list$res.0.4@DEvsRest$`2`$Wstat,
                                                    decreasing = TRUE), ]
cat(rownames(clust1)[1:50])
```

Visualise these genes in violin plots.

**Interpretation**: Now I see that IL2 and IL4 are expressed in more than just cluster 2, but it is nearly always in PMAIO. Cluster 8 is definitely where IL6 is expressed. IL7 is a bit more spread out across treatment types, but it's definitely present in PMAIO in clusters 4, 5, and 11. Cluster 11 is plasma cells, but I'm honestly not sure of 4 and 5 - low signal hepatocytes? IL10 is in clusters 2 and 11 PMAIO. IL12A is a bit more in 4 and 5 PMAIO.

```{r}
VlnPlot(scSeurat, feature = "IL2", split.by = "tissue_type") # Only in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL4", split.by = "tissue_type") # Only in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL6", split.by = "tissue_type") # Stronger in endo and mesem PMAIO
VlnPlot(scSeurat, feature = "IL6-1", split.by = "tissue_type") # No signal
VlnPlot(scSeurat, feature = "IL7", split.by = "tissue_type") # More in PMAIO cluster 4/5
VlnPlot(scSeurat, feature = "IL10", split.by = "tissue_type") # More in PMAIO cluster 2
VlnPlot(scSeurat, feature = "IL12A", split.by = "tissue_type") # A bit more in 1,4,5
VlnPlot(scSeurat, feature = "TGFB1", split.by = "tissue_type") # Pretty even across all
VlnPlot(scSeurat, feature = "TNF", split.by = "tissue_type")
```

Make Violin plots with ggplot

```{r}
genes <- c("IL2","IL4","IL6","IL7","IL10","IL12A","TGFB1","TGFB2","TGFB3","TNF","IL18","IL2RA","CCL5","IFNG","LIF","CCL3L1;CCL3L3;CCL3;CCL18","CCL4L2;CCL4L1;CCL4")
for(gene in genes) {
  vln_df = data.frame(gene = scSeurat[["RNA"]]@data[gene,], 
                      Cluster = Idents(scSeurat), 
                      tissue_type = scSeurat$tissue_type)
  plot <- ggplot(vln_df, aes(x = Cluster, y = gene)) + 
    geom_violin(aes(fill = tissue_type), trim=TRUE, scale = "width") +
    ylab(gene) +
    theme_bw()
  print(plot)
  pdf(file = paste("figures/stimulation/downsampled_vlnPlot_split_", gene, ".pdf", sep = ""))
  print(plot) # Need print function because R doesn't autoprint in loops
  dev.off()
}
```

Looking for more genes

```{r}
gene <- "IL18"
vln_df = data.frame(gene = scSeurat[["RNA"]]@data[gene,], 
                    Cluster = Idents(scSeurat), 
                    tissue_type = scSeurat$tissue_type)
plot <- ggplot(vln_df, aes(x = Cluster, y = gene)) + 
  geom_violin(aes(fill = tissue_type), trim=TRUE, scale = "width") +
  ylab(gene) +
  theme_bw()
print(plot)
```

Perform DE test on T-cells from PMAIO vs unstim T-cells. I see *TNF, IL2RA*, but I also see hepatocyte genes like *ALB-1, STAT3*

```{r}
# Fetch cells to find out relevant cell barcodes
barcode_df <- FetchData(scSeurat, vars = c("tissue_type", "integrated_snn_res.0.4"))
barcode_df$barcode <- rownames(barcode_df)
# Filter on data subsets and pull barcode names
cells1 <- barcode_df %>%
  filter(tissue_type == "6hrs_PMAIO") %>%
  filter(integrated_snn_res.0.4 %in% c(2,6)) %>%
  pull(barcode)
cells2 <- barcode_df %>%
  filter(tissue_type == "6hrs_unstim") %>%
  filter(integrated_snn_res.0.4 %in% c(2,6)) %>%
  pull(barcode)
# Prep for DE testing
scSeurat <- PrepSCTFindMarkers(scSeurat)
# Perform DE test
de_results <- FindMarkers(scSeurat,
            ident.1 = cells1,
            ident.2 = cells2)
cat(row.names(de_results)[1:100], sep = " ")
```


